Normal view
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cs.AI, q-bio.NC updates on arXiv.org
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OntologyAligner: Ontology-Aligned Retrieval and Hierarchy-Guided Large Language Model Reranking for Biomedical Ontology Normalization
arXiv:2609.10055v1 Announce Type: new Abstract: Biomedical ontology normalization maps free-text expressions to standardized concepts, enabling consistent integration and analysis of biomedical data. This task remains challenging because lexical variation and subtle distinctions among hierarchically related concepts can obscure concept boundaries. We present OntologyAligner, a three-stage framework that combines ontology-aligned retrieval, large language model candidate reranking, and selective
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cs.AI, q-bio.NC updates on arXiv.org
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Harbor Adapters and Harbor-Index: Infrastructure and a Curated Meta-Dataset for Large-Scale Agentic Evaluation
arXiv:2609.04298v2 Announce Type: replace Abstract: Evaluating agents on the growing number of agentic benchmarks is challenging because they often require complex environments and agent integrations. We introduce Harbor Adapters, a unified evaluation infrastructure for agentic benchmarks. Our work makes three contributions. First, we develop benchmark adapters that port more than 80 benchmarks to evaluate arbitrary agents, and validate them through rigorous code review and parity experiments.
Harbor Adapters and Harbor-Index: Infrastructure and a Curated Meta-Dataset for Large-Scale Agentic Evaluation
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Pulmonary nodule
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The 2025 lung cancer landscape: advances in screening, molecular taxonomy and therapeutic strategy: a narrative review
Transl Lung Cancer Res. 2026 Mar 23;15(3):62. doi: 10.21037/tlcr-2025-1-1477. Epub 2026 Mar 18.ABSTRACTBACKGROUND AND OBJECTIVE: In 2025, lung cancer research advanced rapidly across the disease continuum, from population-level risk assessment and screening to mechanistic studies of early carcinogenesis and therapeutic innovation in perioperative and metastatic settings. A key shift moved beyond a smoking-centred paradigm toward a multidimensional risk framework reflecting the growing burden amo
The 2025 lung cancer landscape: advances in screening, molecular taxonomy and therapeutic strategy: a narrative review
Transl Lung Cancer Res. 2026 Mar 23;15(3):62. doi: 10.21037/tlcr-2025-1-1477. Epub 2026 Mar 18.
ABSTRACT
BACKGROUND AND OBJECTIVE: In 2025, lung cancer research advanced rapidly across the disease continuum, from population-level risk assessment and screening to mechanistic studies of early carcinogenesis and therapeutic innovation in perioperative and metastatic settings. A key shift moved beyond a smoking-centred paradigm toward a multidimensional risk framework reflecting the growing burden among never-smokers and the roles of air pollution, occupational exposures, and systemic metabolic-inflammatory states. This narrative review aims to synthesize influential 2025 evidence across prevention, diagnosis, treatment, and survivorship, and to identify convergent themes and translational gaps relevant to clinical practice and policy.
METHODS: We performed a narrative synthesis of influential lung cancer studies published in major international journals in 2025. Evidence was organized along a clinically oriented pathway spanning carcinogenesis and screening, precision diagnosis, treatment optimization in resectable and advanced disease, and survivorship, emphasizing practice-informing trials, high-impact translational research, and implementation-relevant technologies.
KEY CONTENT AND FINDINGS: Lineage tracing, single-cell and spatial omics, and evolutionary inference refined concepts of field cancerization, clonal selection, and copy-number-driven fitness. In small-cell lung cancer, evidence further supported neuronal coupling and synapse-like programs as potentially tractable vulnerabilities. Clinically, low-dose computed tomography (CT) strategies and data-informed nodule thresholds aimed to balance under-detection against over-surveillance harms. In diagnostics, artificial intelligence (AI) models increasingly inferred molecular features from routine histopathology ("virtual molecular testing") and should be regarded as decision support requiring prospective validation, population calibration, and explicit failure-mode reporting. Multimodal approaches integrating imaging with circulating tumor DNA (ctDNA) improved feasibility in tissue-limited settings, but clinical utility remains contingent on assay standardization and pathway-level implementation. In resectable disease, longer follow-up consolidated neoadjuvant chemo-immunotherapy for selected patients, while ctDNA kinetics emerged as a candidate biomarker for response-adaptive escalation and de-escalation. In advanced non-small cell lung cancer (NSCLC), phase III evidence for antibody-drug conjugates and bispecific antibodies began reshaping sequencing, while highlighting challenges in toxicity, access, affordability, and immature overall survival in several programs.
CONCLUSIONS: The 2025 landscape reflects coordinated progress in risk conceptualization, biology, diagnostics, and therapeutics, yet gaps in validation, standardization, and real-world deliverability persist. Priorities include prospective evaluation of AI- and ctDNA-enabled pathways, toxicity-informed sequencing, and equitable implementation aligned with health-system capacity.
PMID:41982682 | PMC:PMC13071762 | DOI:10.21037/tlcr-2025-1-1477
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Omics In Lung
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Integrative fragmentomic and mutational signature profile of plasma cfDNA for early lung cancer detection
NPJ Precis Oncol. 2026 Apr 15. doi: 10.1038/s41698-026-01416-y. Online ahead of print.ABSTRACTDetecting lung cancer effectively in the general population is essential for optimizing treatment outcomes and improving the 5-year survival rate. While low-dose computed tomography (LDCT) is the current standard, it has limitations in broader populations. We developed a blood-based multi-omics model using whole-genome cell-free DNA (cfDNA) features to distinguish lung cancer from non-cancer individuals
Integrative fragmentomic and mutational signature profile of plasma cfDNA for early lung cancer detection
NPJ Precis Oncol. 2026 Apr 15. doi: 10.1038/s41698-026-01416-y. Online ahead of print.
ABSTRACT
Detecting lung cancer effectively in the general population is essential for optimizing treatment outcomes and improving the 5-year survival rate. While low-dose computed tomography (LDCT) is the current standard, it has limitations in broader populations. We developed a blood-based multi-omics model using whole-genome cell-free DNA (cfDNA) features to distinguish lung cancer from non-cancer individuals. This study included 1600 patients and an equal number of non-cancer controls, divided into training and validation cohorts. The model achieved an area under the curve (AUC) of 95.59% for the training cohort and 95.74% for the validation cohort. The model consistently performed well across various cancer stages and histological subtypes. To further validate the performance of the model, an external validation cohort was utilized. Notably, it also effectively differentiated non-cancer samples from cancer samples in the external validation cohort, with 85.9% sensitivity and 94.78% specificity. Importantly, in simulated population screenings, our ctDNA assay outperformed both LDCT and a previously established method. This suggests its potential utility in wider lung cancer screening programs, possibly complementing the LDCT approach. In conclusion, our ctDNA assay emerges as a promising and highly sensitive tool for the early detection and categorization of lung cancer.
PMID:41986614 | DOI:10.1038/s41698-026-01416-y
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cs.AI, q-bio.NC updates on arXiv.org
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Finch: Benchmarking Finance & Accounting across Spreadsheet-Centric Enterprise Workflows
arXiv:2512.13168v4 Announce Type: replace Abstract: We introduce FinWorkBench (a.k.a. Finch), a benchmark for evaluating agents on real-world, enterprise-grade finance and accounting workflows that interleave data entry, structuring, formatting, web search, cross-file retrieval, calculation, modeling, validation, translation, visualization, and reporting. Finch is built from authentic enterprise workspaces from Enron (15,000 files and 500,000 emails) and other financial institutions spanning 20
Finch: Benchmarking Finance & Accounting across Spreadsheet-Centric Enterprise Workflows
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Omics In Lung
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Pathogenesis and immune regulation of rheumatoid arthritis-associated interstitial lung disease: from basic research to clinical implications
Front Immunol. 2026 Mar 13;17:1770348. doi: 10.3389/fimmu.2026.1770348. eCollection 2026.ABSTRACTInterstitial lung disease (ILD) is one of the most common extra-articular manifestations of rheumatoid arthritis (RA). Some patients with RA-ILD may develop progressive pulmonary fibrosis, leading to severe impairment of lung function and respiratory failure, which impacts quality of life and can even be life-threatening. This review identified genetic susceptibility, environmental factors, and immun
Pathogenesis and immune regulation of rheumatoid arthritis-associated interstitial lung disease: from basic research to clinical implications
Front Immunol. 2026 Mar 13;17:1770348. doi: 10.3389/fimmu.2026.1770348. eCollection 2026.
ABSTRACT
Interstitial lung disease (ILD) is one of the most common extra-articular manifestations of rheumatoid arthritis (RA). Some patients with RA-ILD may develop progressive pulmonary fibrosis, leading to severe impairment of lung function and respiratory failure, which impacts quality of life and can even be life-threatening. This review identified genetic susceptibility, environmental factors, and immune dysregulation as key contributors to the etiology and pathogenesis of RA-ILD. We highlight that autoantibodies, adaptive immune abnormalities, and tertiary lymphoid organ formation significantly drive pulmonary inflammation and fibrosis, while pro-inflammatory cytokines and epithelial-mesenchymal transition (EMT) further contribute to lung tissue injury. Current treatment options, including glucocorticoids, immunosuppressants, and antifibrotic agents such as nintedanib and pirfenidone, are often limited by substantial side effects. Additionally, emerging therapies like JAK inhibitors, CAR-T cells, and the upcoming phosphodiesterase-4B inhibitor, nerandomilast, show promise, but no curative treatment exists to date. Future research could focus on multi-omics technologies and conducting multicenter clinical trials to establish therapeutic targets and advance precision medicine for RA-ILD.
PMID:41909710 | PMC:PMC13021622 | DOI:10.3389/fimmu.2026.1770348
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cs.AI, q-bio.NC updates on arXiv.org
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AttestLLM: Efficient Attestation Framework for Billion-scale On-device LLMs
arXiv:2509.06326v2 Announce Type: replace-cross Abstract: As on-device LLMs(e.g., Apple on-device Intelligence) are widely adopted to reduce network dependency, improve privacy, and enhance responsiveness, verifying the legitimacy of models running on local devices becomes critical. Existing attestation techniques are not suitable for billion-parameter Large Language Models (LLMs), struggling to remain both time- and memory-efficient while addressing emerging threats in the LLM era. In this pap